Offshore Modeling - Manuscript Model
Adam A. Kemberling
2020-04-23
Manuscript Model
Model Dataset
Model Data - West Only
| Region | N |
|---|---|
| Texas | 3051 |
| LA West | 3656 |
| MS Bight | 1117 |
Total Number of Stations = 7824
Starting in 2000 and continuing through 2018
Total Sapidus Caught was 5468
Overall Frequency of Occurrence was 21.2
Overall Mean Catch Crabs/Hectare: 0.264
Overall Standard Error 0.018
Stations with no catch: 6167 / 7824 Stations or 78.82%
Annual Catch and Occurrence
Data Summary
NOTE: Contains Data Only from Western-Gulf Subset
| Survey Year | Stations | Missing Obs | % Occurrence | Mean Catch | SD | Overdispersed |
|---|---|---|---|---|---|---|
| 2000 | 491 | 0 | 0.1242363 | 0.1434330 | 0.7458628 | yes |
| 2001 | 416 | 0 | 0.1586538 | 0.4066819 | 2.5273291 | yes |
| 2002 | 513 | 0 | 0.2163743 | 0.3070619 | 1.4276630 | yes |
| 2003 | 477 | 0 | 0.2117400 | 0.3260161 | 1.3097278 | yes |
| 2004 | 440 | 0 | 0.1863636 | 0.2700141 | 1.1376114 | yes |
| 2005 | 430 | 0 | 0.3046512 | 0.7326053 | 4.4554998 | yes |
| 2006 | 392 | 0 | 0.2474490 | 0.2941062 | 1.2567796 | yes |
| 2007 | 401 | 0 | 0.2443890 | 0.3713497 | 2.1311305 | yes |
| 2008 | 513 | 0 | 0.1754386 | 0.1034162 | 0.3114427 | no |
| 2009 | 686 | 0 | 0.2172012 | 0.1905500 | 0.6311053 | yes |
| 2010 | 415 | 0 | 0.2554217 | 0.2344566 | 0.6430331 | yes |
| 2011 | 380 | 0 | 0.2842105 | 0.3323709 | 1.0015878 | yes |
| 2012 | 333 | 0 | 0.1561562 | 0.1029894 | 0.3033156 | no |
| 2013 | 274 | 0 | 0.1277372 | 0.0785191 | 0.3293913 | yes |
| 2014 | 349 | 0 | 0.2091691 | 0.2374299 | 1.6983507 | yes |
| 2015 | 350 | 0 | 0.2457143 | 0.2080342 | 0.6744467 | yes |
| 2016 | 322 | 0 | 0.2422360 | 0.1996629 | 0.5809559 | yes |
| 2017 | 335 | 0 | 0.2208955 | 0.2670072 | 0.8739255 | yes |
| 2018 | 307 | 0 | 0.1921824 | 0.1340553 | 0.4087250 | yes |
Annual Mean Catch
Annual Frequency of Occurrence
Side x Side
Region - Season Interactions
NOTE: Contains Data Only from Western-Gulf Subset
NOTE 2: Mean Catch (per hectare) calculated as the average crabs/hectare from each tow within a region-season grouping. Percent occurrence is calculated separately as the average annual percent occurrence for those same groups.
Factor Summary
| Region | Season | Stations | Missing Obs | Mean Catch | SD | Overdispersed |
|---|---|---|---|---|---|---|
| Texas | Summer | 1559 | 0 | 0.2236771 | 0.9768701 | yes |
| Texas | Fall | 1492 | 0 | 0.1062117 | 1.1289038 | yes |
| LA West | Summer | 1874 | 0 | 0.5495995 | 2.6558490 | yes |
| LA West | Fall | 1782 | 0 | 0.1885071 | 0.9017456 | yes |
| MS Bight | Summer | 561 | 0 | 0.2561072 | 1.0760769 | yes |
| MS Bight | Fall | 556 | 0 | 0.0857699 | 0.3310297 | yes |
Average frequency of occurrence for each region and season is calculated in two steps. In the first step the frequency of occurrence for each region and for both survey seasons is calculated for every year. In the second step those annual means are averaged to get an overall measure for each region for each season, and a measure of error around them is calculated to represent the inter-annual variation in the frequency of occurrence.
| Region | Season | N Years | % Occurrence | % Occurrence SE |
|---|---|---|---|---|
| Texas | Summer | 19 | 0.2326514 | 0.0226426 |
| Texas | Fall | 19 | 0.1012512 | 0.0152149 |
| LA West | Summer | 19 | 0.3390328 | 0.0175933 |
| LA West | Fall | 19 | 0.1692615 | 0.0223733 |
| MS Bight | Summer | 19 | 0.2247988 | 0.0341018 |
| MS Bight | Fall | 19 | 0.1329857 | 0.0209576 |
Mean Catch by Region and Season
Frequency of Occurrence
Side x Side
Candidate Models
Model Selection using AIC
| Formulation | AIC | Delta AIC |
|---|---|---|
| no interactions | 13813.95 | 250.2686 |
| year * region | 13671.18 | 107.5012 |
| year * season | 13714.15 | 150.4738 |
| region * season | 13814.66 | 250.9788 |
| Year * region & year * season | 13675.07 | 111.3977 |
| all interactions | 13563.68 | 0.0000 |
Predictor Significance
| Predictor | Df | Deviance | AIC | LRT | Pr(>Chi) |
|---|---|---|---|---|---|
| NA | 3943.099 | 13561.68 | NA | NA | |
| year_f | 18 | 4030.280 | 13612.86 | 87.18098 | 0.0000000 |
| region | 2 | 3964.300 | 13578.88 | 21.20138 | 0.0000249 |
| season | 1 | 3950.663 | 13567.24 | 7.56352 | 0.0059562 |
| year_f:region | 36 | 4102.296 | 13648.87 | 159.19730 | 0.0000000 |
| year_f:season | 18 | 4032.022 | 13614.60 | 88.92312 | 0.0000000 |
| region:season | 2 | 3963.535 | 13578.11 | 20.43597 | 0.0000365 |
Percent Deviance Explained by Best Candidate Model: 22.83
Model Summary
Statistic reported below is the Wald Chi-Square z-score.
| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| (Intercept) | -2.5226968 | 3.318994e-01 | -7.6007882 | 0.0000000 |
| year_f2001 | 1.4475609 | 4.823366e-01 | 3.0011428 | 0.0026897 |
| year_f2002 | 1.2997570 | 4.300605e-01 | 3.0222657 | 0.0025089 |
| year_f2003 | 1.1551077 | 4.338772e-01 | 2.6622921 | 0.0077611 |
| year_f2004 | 0.5951483 | 4.519179e-01 | 1.3169390 | 0.1878591 |
| year_f2005 | 0.8261072 | 4.499882e-01 | 1.8358419 | 0.0663810 |
| year_f2006 | 1.2248743 | 4.363714e-01 | 2.8069538 | 0.0050012 |
| year_f2007 | 0.1928692 | 5.085116e-01 | 0.3792819 | 0.7044785 |
| year_f2008 | -0.0561732 | 4.682622e-01 | -0.1199610 | 0.9045140 |
| year_f2009 | 0.3721793 | 4.157922e-01 | 0.8951087 | 0.3707290 |
| year_f2010 | 1.3678606 | 4.218076e-01 | 3.2428543 | 0.0011834 |
| year_f2011 | 1.6862966 | 4.364890e-01 | 3.8633194 | 0.0001119 |
| year_f2012 | -0.3734306 | 5.004192e-01 | -0.7462355 | 0.4555252 |
| year_f2013 | -1.0190240 | 6.012687e-01 | -1.6947898 | 0.0901153 |
| year_f2014 | 1.7698448 | 4.454852e-01 | 3.9728478 | 0.0000710 |
| year_f2015 | 0.8857008 | 4.505800e-01 | 1.9656906 | 0.0493344 |
| year_f2016 | 1.5388826 | 4.466982e-01 | 3.4450164 | 0.0005710 |
| year_f2017 | 1.4514485 | 4.450963e-01 | 3.2609763 | 0.0011103 |
| year_f2018 | 0.4645462 | 5.119802e-01 | 0.9073519 | 0.3642207 |
| regionLA West | 1.5939088 | 4.110403e-01 | 3.8777434 | 0.0001054 |
| regionMS Bight | -0.5343171 | 6.436653e-01 | -0.8301164 | 0.4064730 |
| seasonFall | -1.6678533 | 6.317096e-01 | -2.6402217 | 0.0082852 |
| year_f2001:regionLA West | -0.0313285 | 6.059282e-01 | -0.0517034 | 0.9587650 |
| year_f2002:regionLA West | -0.7060823 | 5.435910e-01 | -1.2989220 | 0.1939707 |
| year_f2003:regionLA West | -0.3861469 | 5.809924e-01 | -0.6646333 | 0.5062850 |
| year_f2004:regionLA West | -0.1769451 | 5.663152e-01 | -0.3124499 | 0.7546986 |
| year_f2005:regionLA West | 1.0925655 | 5.799504e-01 | 1.8838946 | 0.0595792 |
| year_f2006:regionLA West | -1.1332809 | 5.607124e-01 | -2.0211446 | 0.0432648 |
| year_f2007:regionLA West | -0.4737498 | 6.227672e-01 | -0.7607173 | 0.4468259 |
| year_f2008:regionLA West | -1.3075555 | 5.982034e-01 | -2.1858043 | 0.0288299 |
| year_f2009:regionLA West | -0.5414312 | 5.223652e-01 | -1.0364994 | 0.2999692 |
| year_f2010:regionLA West | -1.3877401 | 5.450823e-01 | -2.5459277 | 0.0108988 |
| year_f2011:regionLA West | -1.4877185 | 5.662343e-01 | -2.6273902 | 0.0086043 |
| year_f2012:regionLA West | -0.2031459 | 6.226694e-01 | -0.3262501 | 0.7442352 |
| year_f2013:regionLA West | 0.1702608 | 7.134430e-01 | 0.2386466 | 0.8113796 |
| year_f2014:regionLA West | -2.2485507 | 5.804815e-01 | -3.8735960 | 0.0001072 |
| year_f2015:regionLA West | -0.9289410 | 5.748246e-01 | -1.6160426 | 0.1060851 |
| year_f2016:regionLA West | -2.0633657 | 5.722598e-01 | -3.6056450 | 0.0003114 |
| year_f2017:regionLA West | -1.0354168 | 5.750724e-01 | -1.8004981 | 0.0717820 |
| year_f2018:regionLA West | -0.9970019 | 6.394455e-01 | -1.5591664 | 0.1189570 |
| year_f2001:regionMS Bight | -1.3446695 | 9.392252e-01 | -1.4316796 | 0.1522355 |
| year_f2002:regionMS Bight | -0.6613078 | 8.518782e-01 | -0.7762938 | 0.4375755 |
| year_f2003:regionMS Bight | 0.7718718 | 8.104769e-01 | 0.9523675 | 0.3409106 |
| year_f2004:regionMS Bight | -0.8048521 | 9.176103e-01 | -0.8771176 | 0.3804227 |
| year_f2005:regionMS Bight | -23.0555869 | 2.509539e+04 | -0.0009187 | 0.9992670 |
| year_f2006:regionMS Bight | 1.5413155 | 7.973287e-01 | 1.9330992 | 0.0532240 |
| year_f2007:regionMS Bight | 2.2531018 | 9.443265e-01 | 2.3859353 | 0.0170357 |
| year_f2008:regionMS Bight | -0.1661901 | 9.549289e-01 | -0.1740340 | 0.8618387 |
| year_f2009:regionMS Bight | 2.2215266 | 7.548809e-01 | 2.9428836 | 0.0032517 |
| year_f2010:regionMS Bight | 0.6176639 | 9.930385e-01 | 0.6219939 | 0.5339459 |
| year_f2011:regionMS Bight | -0.8426081 | 1.008287e+00 | -0.8356832 | 0.4033331 |
| year_f2012:regionMS Bight | 0.7996533 | 1.078004e+00 | 0.7417906 | 0.4582142 |
| year_f2013:regionMS Bight | 2.1630663 | 1.103177e+00 | 1.9607617 | 0.0499068 |
| year_f2014:regionMS Bight | -0.1870077 | 9.558497e-01 | -0.1956455 | 0.8448877 |
| year_f2015:regionMS Bight | -0.8365878 | 1.101368e+00 | -0.7595896 | 0.4474999 |
| year_f2016:regionMS Bight | -2.3816120 | 1.343394e+00 | -1.7728324 | 0.0762565 |
| year_f2017:regionMS Bight | 0.5368907 | 9.321358e-01 | 0.5759791 | 0.5646293 |
| year_f2018:regionMS Bight | 0.6299970 | 1.058362e+00 | 0.5952567 | 0.5516719 |
| year_f2001:seasonFall | -1.0831173 | 8.627183e-01 | -1.2554703 | 0.2093081 |
| year_f2002:seasonFall | -0.7111307 | 8.144259e-01 | -0.8731681 | 0.3825715 |
| year_f2003:seasonFall | 1.0883988 | 7.521976e-01 | 1.4469586 | 0.1479085 |
| year_f2004:seasonFall | 0.0545197 | 8.184878e-01 | 0.0666102 | 0.9468920 |
| year_f2005:seasonFall | -0.1411545 | 8.121687e-01 | -0.1737994 | 0.8620231 |
| year_f2006:seasonFall | -1.3370576 | 9.126945e-01 | -1.4649564 | 0.1429328 |
| year_f2007:seasonFall | 3.9099502 | 7.882960e-01 | 4.9600027 | 0.0000007 |
| year_f2008:seasonFall | 1.4697352 | 8.113272e-01 | 1.8115196 | 0.0700605 |
| year_f2009:seasonFall | 0.1199549 | 7.775887e-01 | 0.1542652 | 0.8774007 |
| year_f2010:seasonFall | -0.0969826 | 7.845550e-01 | -0.1236148 | 0.9016202 |
| year_f2011:seasonFall | 0.6176497 | 7.585877e-01 | 0.8142100 | 0.4155246 |
| year_f2012:seasonFall | 1.8216675 | 8.465341e-01 | 2.1519128 | 0.0314042 |
| year_f2013:seasonFall | 0.8779331 | 1.123718e+00 | 0.7812751 | 0.4346407 |
| year_f2014:seasonFall | 0.1221161 | 7.897130e-01 | 0.1546335 | 0.8771102 |
| year_f2015:seasonFall | 1.2693958 | 7.855777e-01 | 1.6158756 | 0.1061212 |
| year_f2016:seasonFall | 0.8072051 | 8.013457e-01 | 1.0073119 | 0.3137849 |
| year_f2017:seasonFall | -0.5217648 | 8.335876e-01 | -0.6259267 | 0.5313630 |
| year_f2018:seasonFall | 0.7942303 | 8.601640e-01 | 0.9233475 | 0.3558261 |
| regionLA West:seasonFall | -1.4273364 | 8.168868e-01 | -1.7472879 | 0.0805874 |
| regionMS Bight:seasonFall | 2.6392913 | 9.572109e-01 | 2.7572727 | 0.0058286 |
| year_f2001:regionLA West:seasonFall | 1.0743927 | 1.085168e+00 | 0.9900709 | 0.3221395 |
| year_f2002:regionLA West:seasonFall | 2.8183202 | 1.022460e+00 | 2.7564122 | 0.0058439 |
| year_f2003:regionLA West:seasonFall | 1.1596534 | 9.934722e-01 | 1.1672731 | 0.2431001 |
| year_f2004:regionLA West:seasonFall | 2.2717123 | 1.033221e+00 | 2.1986708 | 0.0279013 |
| year_f2005:regionLA West:seasonFall | 1.6319522 | 1.027383e+00 | 1.5884555 | 0.1121834 |
| year_f2006:regionLA West:seasonFall | 3.1233229 | 1.191337e+00 | 2.6216954 | 0.0087494 |
| year_f2007:regionLA West:seasonFall | -1.3797323 | 1.016559e+00 | -1.3572576 | 0.1746994 |
| year_f2008:regionLA West:seasonFall | 2.1041048 | 1.028964e+00 | 2.0448778 | 0.0408669 |
| year_f2009:regionLA West:seasonFall | 1.2507351 | 9.999241e-01 | 1.2508301 | 0.2109965 |
| year_f2010:regionLA West:seasonFall | 2.1773613 | 1.014205e+00 | 2.1468653 | 0.0318040 |
| year_f2011:regionLA West:seasonFall | 2.1129189 | 9.932891e-01 | 2.1271943 | 0.0334039 |
| year_f2012:regionLA West:seasonFall | -0.3379970 | 1.119827e+00 | -0.3018295 | 0.7627820 |
| year_f2013:regionLA West:seasonFall | 0.9674971 | 1.378100e+00 | 0.7020516 | 0.4826470 |
| year_f2014:regionLA West:seasonFall | 2.6464584 | 1.028604e+00 | 2.5728655 | 0.0100860 |
| year_f2015:regionLA West:seasonFall | 0.9123447 | 1.028351e+00 | 0.8871919 | 0.3749756 |
| year_f2016:regionLA West:seasonFall | 0.8770735 | 1.070046e+00 | 0.8196597 | 0.4124102 |
| year_f2017:regionLA West:seasonFall | 0.6889676 | 1.122341e+00 | 0.6138667 | 0.5393034 |
| year_f2018:regionLA West:seasonFall | 1.5625355 | 1.098167e+00 | 1.4228583 | 0.1547772 |
| year_f2001:regionMS Bight:seasonFall | -0.6658444 | 1.471203e+00 | -0.4525850 | 0.6508476 |
| year_f2002:regionMS Bight:seasonFall | -0.6443478 | 1.294920e+00 | -0.4975966 | 0.6187684 |
| year_f2003:regionMS Bight:seasonFall | -4.9358899 | 1.276094e+00 | -3.8679664 | 0.0001097 |
| year_f2004:regionMS Bight:seasonFall | 0.2358027 | 1.624922e+00 | 0.1451163 | 0.8846191 |
| year_f2005:regionMS Bight:seasonFall | 23.4467784 | 2.509539e+04 | 0.0009343 | 0.9992545 |
| year_f2006:regionMS Bight:seasonFall | -1.8844192 | 1.315935e+00 | -1.4319998 | 0.1521439 |
| year_f2007:regionMS Bight:seasonFall | -6.4670075 | 1.329080e+00 | -4.8657767 | 0.0000011 |
| year_f2008:regionMS Bight:seasonFall | -2.6549459 | 1.396063e+00 | -1.9017371 | 0.0572055 |
| year_f2009:regionMS Bight:seasonFall | -4.2973049 | 1.285840e+00 | -3.3420225 | 0.0008317 |
| year_f2010:regionMS Bight:seasonFall | -2.4745921 | 1.491515e+00 | -1.6591135 | 0.0970929 |
| year_f2011:regionMS Bight:seasonFall | -2.6720578 | 1.582227e+00 | -1.6887952 | 0.0912587 |
| year_f2012:regionMS Bight:seasonFall | -2.6213922 | 1.639367e+00 | -1.5990273 | 0.1098145 |
| year_f2013:regionMS Bight:seasonFall | -3.4408723 | 1.983350e+00 | -1.7348794 | 0.0827622 |
| year_f2014:regionMS Bight:seasonFall | -2.9338609 | 1.558110e+00 | -1.8829614 | 0.0597056 |
| year_f2015:regionMS Bight:seasonFall | -3.2090400 | 1.796716e+00 | -1.7860585 | 0.0740898 |
| year_f2016:regionMS Bight:seasonFall | -23.4575078 | 4.058982e+04 | -0.0005779 | 0.9995389 |
| year_f2017:regionMS Bight:seasonFall | -1.9693608 | 1.485972e+00 | -1.3253011 | 0.1850713 |
| year_f2018:regionMS Bight:seasonFall | -2.3765912 | 1.608082e+00 | -1.4779040 | 0.1394335 |
Interaction Plots
Tukey HSD multiple comparison test
Test 1. Region
##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: MASS:::glm.nb(formula = sapidus_catch ~ year_f * region * season +
## offset(log(area_hectares)), data = seamap_west, init.theta = 0.174655286,
## link = log)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## LA West - Texas == 0 1.5939 0.4110 3.878 0.000297 ***
## MS Bight - Texas == 0 -0.5343 0.6437 -0.830 0.678372
## MS Bight - LA West == 0 -2.1282 0.6024 -3.533 0.001058 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Test 2. Year
##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: MASS:::glm.nb(formula = sapidus_catch ~ year_f * region * season +
## offset(log(area_hectares)), data = seamap_west, init.theta = 0.174655286,
## link = log)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Fall - Summer == 0 -1.6679 0.6317 -2.64 0.00829 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Catch per Hectare Plot
Seasonal Prediction Differences
Observed vs. Predicted Data
Original
Predictions Only
Observed Only
Raster Plots
NOTE: Contains Data Only from Western-Gulf Subset
Statistical Zones
Sampling Effort
Catch per Hectare
Variance in CPUE
Total Catch
Outlining Cells with Geom_Tile
Study Area Size From Convex Hull
## [1] "Area of Analysis Data Study Area (raster): 122297.8 km2"## [1] "Area of Analysis Data Study Area (raster): 12229780 Hectares"